Calcium in PDB 8jx9: Rat Megalin Bodya

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Calcium atom in the Rat Megalin Bodya (pdb code 8jx9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 20 binding sites of Calcium where determined in the Rat Megalin Bodya, PDB code: 8jx9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 20 in the Rat Megalin Bodya


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rat Megalin Bodya within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4708 b:126.7 occ:1.00 OD1 B:ASP1252 2.3 142.4 1.0 OD2 B:ASP1256 2.3 116.8 1.0 O B:TRP1249 2.3 112.2 1.0 O B:HIS1254 2.4 122.4 1.0 OD2 B:ASP1262 2.8 123.6 1.0 OE2 B:GLU1263 3.0 137.2 1.0 CD B:GLU1263 3.2 138.0 1.0 CG B:ASP1252 3.3 142.3 1.0 CG B:ASP1256 3.4 117.1 1.0 OE1 B:GLU1263 3.5 137.0 1.0 C B:TRP1249 3.5 108.6 1.0 C B:HIS1254 3.5 120.6 1.0 CG B:ASP1262 3.7 125.3 1.0 OD2 B:ASP1252 3.8 141.6 1.0 CG B:GLU1263 3.9 137.9 1.0 CB B:ASP1262 4.0 124.9 1.0 N B:ASP1252 4.0 137.3 1.0 N B:ASP1256 4.1 113.7 1.0 N B:HIS1254 4.1 118.0 1.0 CA B:GLU1250 4.1 126.9 1.0 N B:CYS1251 4.1 143.6 1.0 CB B:ASP1256 4.2 116.9 1.0 N B:GLU1250 4.3 123.5 1.0 CB B:ASP1252 4.3 139.9 1.0 OD1 B:ASP1256 4.3 118.4 1.0 CA B:HIS1254 4.3 118.6 1.0 C B:GLU1250 4.4 127.7 1.0 O B:ASP1262 4.4 125.2 1.0 N B:PRO1255 4.5 117.0 1.0 CA B:TRP1249 4.6 109.6 1.0 CA B:PRO1255 4.6 118.8 1.0 CA B:ASP1252 4.6 137.8 1.0 N B:GLY1253 4.7 128.8 1.0 C B:ASP1262 4.7 124.4 1.0 C B:PRO1255 4.7 121.4 1.0 CA B:ASP1256 4.8 114.5 1.0 CB B:HIS1254 4.8 116.7 1.0 CB B:TRP1249 4.8 109.8 1.0 OD1 B:ASP1262 4.9 124.1 1.0 C B:ASP1252 4.9 137.1 1.0 CA B:CYS1251 4.9 145.8 1.0 C B:CYS1251 5.0 144.1 1.0

Calcium binding site 2 out of 20 in the Rat Megalin Bodya


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rat Megalin Bodya within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4709 b:331.0 occ:1.00 OD1 B:ASP2928 2.3 318.8 1.0 OD2 B:ASP2938 2.3 325.5 1.0 OE2 B:GLU2939 2.4 323.8 1.0 O B:ASP2930 2.4 318.4 1.0 O B:TRP2925 2.4 320.6 1.0 OD2 B:ASP2932 2.5 326.0 1.0 CG B:ASP2928 3.1 318.2 1.0 CD B:GLU2939 3.3 323.4 1.0 CG B:ASP2938 3.4 325.4 1.0 N B:ASP2928 3.5 318.4 1.0 CG B:GLU2939 3.5 323.4 1.0 C B:ASP2930 3.6 318.0 1.0 CG B:ASP2932 3.6 325.7 1.0 C B:TRP2925 3.6 320.1 1.0 N B:CYS2927 3.7 318.5 1.0 OD2 B:ASP2928 3.7 317.8 1.0 OD1 B:ASP2938 3.8 325.5 1.0 N B:ASP2932 4.0 326.1 1.0 CB B:ASP2932 4.0 325.8 1.0 CB B:ASP2928 4.1 317.9 1.0 N B:ASP2930 4.1 318.5 1.0 C B:VAL2926 4.2 318.6 1.0 CA B:ASP2928 4.2 318.1 1.0 CA B:VAL2926 4.3 318.4 1.0 CA B:CYS2927 4.3 318.4 1.0 O B:ASP2938 4.3 325.0 1.0 C B:CYS2927 4.4 318.4 1.0 N B:VAL2926 4.4 318.5 1.0 N B:GLY2929 4.4 316.6 1.0 OE1 B:GLU2939 4.5 323.1 1.0 CA B:ASP2930 4.5 318.1 1.0 N B:ASN2931 4.5 321.3 1.0 C B:ASN2931 4.5 321.7 1.0 CB B:TRP2925 4.5 320.1 1.0 CA B:ASN2931 4.5 321.4 1.0 CB B:ASP2938 4.6 325.1 1.0 CA B:ASP2932 4.6 326.1 1.0 CA B:TRP2925 4.6 319.9 1.0 C B:ASP2928 4.7 318.1 1.0 OD1 B:ASP2932 4.7 325.3 1.0 C B:ASP2938 4.9 325.1 1.0 CB B:GLU2939 5.0 323.3 1.0

Calcium binding site 3 out of 20 in the Rat Megalin Bodya


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rat Megalin Bodya within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4710 b:298.3 occ:1.00 OD2 B:ASP2979 2.3 284.0 1.0 OE2 B:GLU2986 2.3 284.4 1.0 OD1 B:ASP2975 2.3 284.2 1.0 O B:ASP2977 2.4 283.2 1.0 OD2 B:ASP2985 2.6 281.4 1.0 O B:TRP2972 2.6 281.3 1.0 CG B:ASP2979 2.6 283.8 1.0 OD1 B:ASP2979 2.6 284.1 1.0 CG B:ASP2975 3.4 283.2 1.0 C B:ASP2977 3.4 282.3 1.0 CD B:GLU2986 3.4 283.3 1.0 C B:TRP2972 3.8 281.2 1.0 CG B:ASP2985 3.8 280.8 1.0 N B:ASP2977 3.8 282.1 1.0 CB B:ASP2979 3.8 283.4 1.0 N B:ASP2979 3.9 284.0 1.0 CA B:ASP2977 4.0 281.8 1.0 N B:ASP2975 4.0 283.5 1.0 OD2 B:ASP2975 4.0 282.6 1.0 CB B:ASP2977 4.1 282.0 1.0 N B:CYS2974 4.2 284.4 1.0 CG B:GLU2986 4.2 282.6 1.0 OE1 B:GLU2986 4.3 282.9 1.0 CA B:VAL2973 4.3 281.3 1.0 CB B:ASP2975 4.4 283.0 1.0 N B:VAL2973 4.5 281.6 1.0 CA B:ASP2979 4.5 283.3 1.0 N B:ALA2978 4.5 281.0 1.0 CB B:TRP2972 4.5 281.3 1.0 C B:VAL2973 4.5 281.7 1.0 CA B:ASP2975 4.6 283.3 1.0 OD1 B:ASP2985 4.6 280.5 1.0 N B:GLY2976 4.6 282.5 1.0 CB B:ASP2985 4.7 280.4 1.0 CA B:TRP2972 4.8 281.7 1.0 C B:ALA2978 4.9 281.6 1.0 CG B:TRP2972 4.9 281.1 1.0 CD1 B:TRP2972 4.9 281.2 1.0 C B:ASP2975 4.9 283.3 1.0 CA B:ALA2978 4.9 281.0 1.0 C B:CYS2974 4.9 283.3 1.0 CA B:CYS2974 5.0 283.6 1.0 C B:GLY2976 5.0 282.0 1.0

Calcium binding site 4 out of 20 in the Rat Megalin Bodya


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rat Megalin Bodya within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4711 b:188.5 occ:1.00 OE2 B:GLU3026 2.3 183.3 1.0 OD1 B:ASP3015 2.3 184.6 1.0 OD2 B:ASP3019 2.3 204.7 1.0 OD2 B:ASP3025 2.3 186.5 1.0 O B:ARG3017 2.4 183.1 1.0 O B:PHE3012 2.6 200.9 1.0 CG B:ASP3015 3.0 185.7 1.0 OD2 B:ASP3015 3.0 186.2 1.0 CD B:GLU3026 3.2 184.0 1.0 C B:PHE3012 3.3 200.4 1.0 CG B:ASP3025 3.3 187.2 1.0 CG B:ASP3019 3.4 203.1 1.0 C B:ARG3017 3.5 182.8 1.0 CB B:ASP3025 3.8 188.4 1.0 CG B:GLU3026 3.9 184.0 1.0 N B:ARG3013 3.9 191.2 1.0 CA B:ARG3013 4.0 190.0 1.0 CB B:ASP3019 4.0 201.8 1.0 OE1 B:GLU3026 4.1 182.6 1.0 N B:ASP3019 4.1 200.9 1.0 N B:ARG3017 4.1 184.3 1.0 CA B:PHE3012 4.1 200.6 1.0 CA B:ARG3017 4.1 182.7 1.0 CB B:ARG3017 4.2 183.3 1.0 OD1 B:ASP3025 4.3 186.8 1.0 CB B:ASP3015 4.4 186.9 1.0 N B:ASP3015 4.4 185.4 1.0 C B:ARG3013 4.4 191.3 1.0 OD1 B:ASP3019 4.4 200.9 1.0 CB B:PHE3012 4.5 200.9 1.0 N B:CYS3014 4.5 188.8 1.0 N B:ASN3018 4.6 193.8 1.0 CA B:ASP3019 4.7 201.2 1.0 CA B:ASP3015 4.8 185.7 1.0 N B:GLU3026 4.8 183.4 1.0 C B:ASP3015 5.0 185.9 1.0 CA B:ASN3018 5.0 195.5 1.0 C B:ASP3025 5.0 187.9 1.0

Calcium binding site 5 out of 20 in the Rat Megalin Bodya


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Rat Megalin Bodya within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4712 b:187.1 occ:1.00 OE2 B:GLU3065 2.3 183.3 1.0 OD1 B:ASP3054 2.3 178.3 1.0 OD2 B:ASP3064 2.3 182.2 1.0 OD2 B:ASP3058 2.3 176.9 1.0 O B:PHE3051 2.3 181.4 1.0 CG B:ASP3054 2.7 178.0 1.0 OD2 B:ASP3054 2.8 177.4 1.0 O B:ASP3056 2.9 182.3 1.0 C B:PHE3051 3.4 181.0 1.0 CG B:ASP3058 3.4 176.5 1.0 CD B:GLU3065 3.4 183.0 1.0 CG B:ASP3064 3.5 182.2 1.0 N B:ASP3054 3.6 180.1 1.0 N B:CYS3053 3.8 173.2 1.0 CB B:ASP3054 3.9 178.2 1.0 C B:ASP3056 4.0 182.6 1.0 C B:VAL3052 4.1 173.6 1.0 CA B:VAL3052 4.1 174.1 1.0 CA B:ASP3054 4.2 179.8 1.0 N B:ASP3056 4.2 182.5 1.0 N B:VAL3052 4.2 175.2 1.0 CG B:GLU3065 4.2 181.0 1.0 CB B:ASP3064 4.2 180.2 1.0 CB B:ASP3058 4.3 176.9 1.0 OD1 B:ASP3058 4.3 177.0 1.0 OE1 B:GLU3065 4.3 183.4 1.0 CA B:PHE3051 4.3 180.2 1.0 OD1 B:ASP3064 4.4 182.8 1.0 CA B:ASP3056 4.4 183.2 1.0 C B:ASP3054 4.5 179.4 1.0 C B:CYS3053 4.5 174.1 1.0 CD1 B:PHE3051 4.5 179.6 1.0 CB B:ASP3056 4.5 183.5 1.0 N B:ASP3058 4.5 177.5 1.0 CB B:PHE3051 4.5 178.4 1.0 CA B:CYS3053 4.6 173.5 1.0 O B:ASP3064 4.6 182.9 1.0 N B:GLU3055 4.7 184.8 1.0 O B:VAL3052 4.8 174.2 1.0 C B:ASP3064 4.9 181.0 1.0

Calcium binding site 6 out of 20 in the Rat Megalin Bodya


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Rat Megalin Bodya within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4713 b:280.0 occ:1.00 OD1 B:ASN3097 2.2 259.8 1.0 OE1 B:GLU3108 2.3 263.3 1.0 OD2 B:ASP3107 2.3 268.2 1.0 OD2 B:ASP3101 2.3 266.8 1.0 OE2 B:GLU3108 2.7 263.2 1.0 CD B:GLU3108 2.8 263.1 1.0 O B:ARG3094 3.0 256.8 1.0 O B:VAL3099 3.0 263.1 1.0 CG B:ASN3097 3.0 258.8 1.0 CG B:ASP3107 3.3 267.5 1.0 CG B:ASP3101 3.5 266.3 1.0 ND2 B:ASN3097 3.5 258.8 1.0 N B:ASN3097 3.6 259.2 1.0 CB B:ASP3107 3.7 266.4 1.0 CB B:ASN3097 4.1 258.2 1.0 N B:CYS3096 4.1 256.8 1.0 C B:VAL3099 4.1 263.2 1.0 C B:ARG3094 4.2 256.1 1.0 CG B:GLU3108 4.2 262.4 1.0 CA B:ASN3097 4.3 258.7 1.0 CB B:ASP3101 4.3 266.2 1.0 N B:HIS3098 4.3 260.1 1.0 N B:VAL3099 4.3 264.4 1.0 OD1 B:ASP3107 4.4 267.7 1.0 OD1 B:ASP3101 4.4 266.1 1.0 CD1 B:ILE3090 4.5 252.2 1.0 C B:CYS3096 4.5 257.1 1.0 N B:ASP3101 4.5 266.6 1.0 CA B:CYS3096 4.5 256.9 1.0 C B:ASN3097 4.6 259.6 1.0 C B:ASP3107 4.6 266.4 1.0 C B:VAL3095 4.7 252.5 1.0 O B:ASP3107 4.7 265.7 1.0 CB B:ARG3094 4.8 256.3 1.0 CA B:ASP3107 4.8 266.6 1.0 CA B:VAL3099 4.8 263.6 1.0 N B:GLU3108 4.9 263.1 1.0 CA B:VAL3095 4.9 252.1 1.0

Calcium binding site 7 out of 20 in the Rat Megalin Bodya


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Rat Megalin Bodya within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4714 b:127.9 occ:1.00 O B:VAL3172 2.3 123.8 1.0 OE1 B:GLU3157 2.3 130.0 1.0 OE2 B:GLU3157 2.4 128.3 1.0 OD1 B:ASP3154 2.5 138.8 1.0 CD B:GLU3157 2.7 129.0 1.0 O B:ILE3155 2.7 132.8 1.0 OD1 B:ASN3171 2.7 125.9 1.0 O B:SER3175 2.7 120.1 1.0 OD2 B:ASP3154 3.0 142.6 1.0 CG B:ASP3154 3.1 140.5 1.0 N B:SER3175 3.4 114.6 1.0 C B:VAL3172 3.5 123.1 1.0 C B:SER3175 3.6 120.3 1.0 N B:GLY3174 3.6 136.5 1.0 CG B:ASN3171 3.8 126.9 1.0 C B:ILE3155 3.9 132.8 1.0 CA B:SER3175 4.0 113.3 1.0 C B:GLY3174 4.0 135.1 1.0 N B:VAL3172 4.0 126.7 1.0 CG B:GLU3157 4.2 124.7 1.0 CA B:GLY3174 4.2 134.9 1.0 ND2 B:ASN3171 4.3 128.6 1.0 CA B:VAL3172 4.4 124.5 1.0 C B:VAL3173 4.4 128.7 1.0 N B:VAL3173 4.5 127.6 1.0 CA B:VAL3173 4.5 129.9 1.0 N B:ILE3155 4.5 129.4 1.0 N B:GLU3157 4.5 122.7 1.0 CB B:ASP3154 4.6 138.2 1.0 O B:GLY3142 4.7 136.8 1.0 N B:TYR3176 4.8 111.7 1.0 N B:ASP3156 4.8 128.9 1.0 CA B:ASP3156 4.8 125.5 1.0 CA B:ILE3155 4.8 130.1 1.0 O B:GLY3174 4.9 139.7 1.0 C B:ASP3154 5.0 138.3 1.0

Calcium binding site 8 out of 20 in the Rat Megalin Bodya


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Rat Megalin Bodya within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4715 b:91.4 occ:1.00 OD1 B:ASP3294 2.3 104.3 1.0 O B:ALA3291 2.4 85.2 1.0 O B:GLU3323 2.5 94.2 1.0 CG B:ASP3294 3.1 103.5 1.0 OD2 B:ASP3294 3.2 102.3 1.0 C B:ALA3291 3.5 83.4 1.0 C B:GLU3323 3.7 98.2 1.0 O B:PHE3322 4.0 93.0 1.0 CA B:ILE3292 4.3 96.0 1.0 N B:ILE3292 4.4 99.3 1.0 CA B:GLU3323 4.4 102.0 1.0 CB B:ASP3294 4.4 104.0 1.0 O B:ILE3292 4.4 95.3 1.0 CA B:ALA3291 4.5 85.5 1.0 C B:ILE3292 4.7 91.1 1.0 N B:HIS3324 4.7 85.6 1.0 CD B:PRO3325 4.8 70.3 1.0 CA B:HIS3324 4.9 84.7 1.0 CA B:ASP3294 4.9 99.4 1.0 CB B:ALA3291 5.0 80.9 1.0

Calcium binding site 9 out of 20 in the Rat Megalin Bodya


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Rat Megalin Bodya within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4716 b:92.6 occ:1.00 OE1 B:GLU3367 2.4 91.2 1.0 O B:VAL3344 3.0 96.5 1.0 CD B:GLU3367 3.4 91.2 1.0 OE2 B:GLU3367 3.8 93.3 1.0 OG1 B:THR3684 3.9 111.6 1.0 C B:VAL3344 4.0 93.6 1.0 OE1 B:GLU3685 4.4 122.5 1.0 CA B:VAL3344 4.5 92.0 1.0 CB B:THR3684 4.5 113.1 1.0 CG B:GLU3367 4.7 85.5 1.0 CG2 B:VAL3344 4.8 95.4 1.0 O B:GLY3343 4.8 102.4 1.0 O B:ILE3366 4.8 90.7 1.0 CA B:GLU3367 4.9 82.3 1.0 CB B:GLU3367 5.0 84.7 1.0

Calcium binding site 10 out of 20 in the Rat Megalin Bodya


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Rat Megalin Bodya within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4717 b:113.5 occ:1.00 O B:ALA3386 2.3 76.0 1.0 O B:PRO3410 2.5 84.0 1.0 O B:HIS3387 3.2 92.3 1.0 C B:ALA3386 3.4 70.7 1.0 C B:PRO3410 3.7 73.5 1.0 CA B:HIS3387 3.7 80.1 1.0 C B:HIS3387 3.8 83.4 1.0 N B:HIS3387 4.0 78.9 1.0 O B:LEU3409 4.2 91.3 1.0 CA B:PRO3410 4.4 75.3 1.0 N B:GLY3389 4.6 67.8 1.0 N B:HIS3411 4.6 67.5 1.0 CA B:ALA3386 4.6 69.9 1.0 CA B:GLY3389 4.7 72.4 1.0 CA B:HIS3411 4.8 66.9 1.0 ND2 B:ASN3428 4.9 81.1 1.0 N B:LEU3388 4.9 68.2 1.0

S.Goto, A.Tsutsumi, Y.Lee, M.Hosojima, H.Kabasawa, K.Komochi, S.Nagatoishi, K.Takemoto, K.Tsumoto, T.Nishizawa, M.Kikkawa, A.Saito. Cryo-Em Structures Elucidate the Multiligand Receptor Nature of Megalin. Proc.Natl.Acad.Sci.Usa V. 121 59121 2024.
ISSN: ESSN 1091-6490
PubMed: 38771880
DOI: 10.1073/PNAS.2318859121